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'X-ray crystal Structure of the putative N-type ATP pyrophosphatase (PF0828) in complex with ATP from Pyrococcus furiosus, Northeast Structural Genomics Consortium Target PfR23
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3RJZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 291 Protein solution: 10 mM Tris (pH 7.5), 100 mM sodium chloride, 5 mM DTT, 0.02% NaN3, and 5mM ATP. Reservoir solution: 100mM Tris (pH 8.5), 300mM (NH4)HPO4 and 1% (w/v) PEG8000., VAPOR DIFFUSION, SITTING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.44 49.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.979 α = 90 b = 64.072 β = 90 c = 140.134 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 4 mirrors 2008-09-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X4A 0.97905 NSLS X4A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.3 30 98.3 0.085 0.068 15 3.7 45876 45097 12.6
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.3 2.38 91.8 0.331 0.296 2.9 3.3 4201
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) Cut-off Sigma (F) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3RJZ 2.3 19.88 2 2 45515 37778 3683 83 0.213 0.203 0.203 0.2162 0.253 0.2634 RANDOM 28
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] -2.13 6.92 -4.79
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 23.1 c_angle_deg 1.3 c_improper_angle_d 0.69 c_bond_d 0.008 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 23.1 c_angle_deg 1.3 c_improper_angle_d 0.69 c_bond_d 0.008 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d_na c_improper_angle_d_prot c_mcbond_it c_mcangle_it c_scbond_it c_scangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3516 Nucleic Acid Atoms Solvent Atoms 162 Heterogen Atoms 77
Software Software Software Name Purpose ADSC data collection COMO phasing CNS refinement DENZO data reduction SCALEPACK data scaling